Genome Wide Association Study Using Copy-Number Variants in Medicago truncatula

Medicago truncatula is a model legume often used to study the symbiosis between legumes and nitrogen-fixing rhizobia. M. truncatula has a stable, high-quality reference genome and a well characterized collection of HapMap accessions, for which SNPs have been called through deep re-sequencing. In this study we have identified copy-number variants (CNVs) in M. truncatula HapMap accessions and performed a genome-wide association study (GWAS) on nodulation-related traits. CNVs were identified through comparison between reference read-depth and specific accession read-depths. Polymorphisms were then treated as SNP markers in combination with the published Medicago HapMap SNPs. An association analyses conducted with TASSEL using this combined set of variants identified a CNV (a deletion relative to the reference genome) of a nodule-related cysteine-rich (NCR) peptide that is associated with a reduction of total nodule count. This NCR deletion was validated by comparison to de novo assemblies. The observed CNV events had not been tagged previously by SNP calls and are in low LD with nearby SNPs. These results indicate that CNVs may play a role in phenotypic variation that has not been properly characterized by SNP-only methods, and hints that other structural variants may also play an important role in phenotype. This work was supported by NSF Plant Genome grant IOS-1237993.